Yeast flocculation: New story in fuel ethanol production

Physiological responses contributing to multiple stress tolerance in Pichia kudriavzevii with potential enhancement for ethanol fermentation

Economically feasible ethanol production requires efficient hydrolysis of lignocellulosic biomass and high-temperature processing to enable simultaneous saccharification and fermentation. During the lignocellulolysic hydrolysate, the yeast must encounter with a multiple of inhibitors such as heat and furfural. To solve this problem, a potential fermentative yeast strain that tolerated simultaneous multistress and enhance ethanol concentration was investigated. Twenty yeast isolates were classified into two major yeast species, namely Pichia kudriavzevii (twelve isolates) and Candida tropicalis (eight isolates). All P. kudriavzevii isolates were able to grow at high temperature (45 °C) and exhibited stress tolerance toward furfural. Among P. kudriavzevii isolates, NUCG-S3 presented the highest specific growth rate under each stress condition of heat and furfural, and multistress. Morphological changes in P. kudriavzevii isolates (NUCG-S2, NUCG-S3, NUKL-P1, NUKL-P3, and NUOR-J1) showed alteration in mean cell length and width compared to the non-stress condition. Ethanol production by glucose was also determined. The yeast strain, NUCG-S3, gave the highest ethanol concentrations at 99.46 ± 0.82, 62.23 ± 0.96, and 65.80 ± 0.62 g/l (P < 0.05) under temperature of 30 °C, 40 °C, and 42 °C, respectively. The tolerant isolated yeast NUCG-S3 achieved ethanol production of 53.58 ± 3.36 and 48.06 ± 3.31 g/l (P < 0.05) in the presence of 15 mM furfural and multistress (42 °C with 15 mM furfural), respectively. Based on the results of the present study, the novel thermos and furfural-tolerant yeast strain P. kudriavzevii NUCG-S3 showed promise as a highly proficient yeast for high-temperature ethanol fermentation.

Comparative responses of flocculating and nonflocculating yeasts to cell density and chemical stress in lactic acid fermentation

While flocculation has demonstrated its efficacy in enhancing yeast robustness and ethanol production, its potential application for lactic acid fermentation remains largely unexplored. Our study examined the differences between flocculating and nonflocculating Saccharomyces cerevisiae strains in terms of their metabolic dynamics when incorporating an exogenous lactic acid pathway, across varying cell densities and in the presence of lignocellulose-derived byproducts. Comparative gene expression profiles revealed that cultivating a nonflocculant strain at higher cell density yielded a substantial upregulation of genes associated with glycolysis, energy metabolism, and other key pathways, resulting in elevated levels of fermentation products. Meanwhile, the flocculating strain displayed an inherent ability to sustain high glycolytic activity regardless of the cell density. Moreover, our investigation revealed a significant reduction in glycolytic activity under chemical stress, potentially attributable to diminished ATP supply during the energy investment phase. Conversely, the formation of flocs in the flocculating strain conferred protection against toxic chemicals present in the medium, fostering more stable lactic acid production levels. Additionally, the distinct flocculation traits observed between the two examined strains may be attributed to variations in the nucleotide sequences of the flocculin genes and their regulators. This study uncovers the potential of flocculation for enhanced lactic acid production in yeast, offering insights into metabolic mechanisms and potential gene targets for strain improvement.

Intracellular accumulation of c-di-GMP and its regulation on self-flocculation of the bacterial cells of Zymomonas mobilis

Zymomonas mobilis is an emerging chassis for being engineered to produce bulk products due to its unique glycolysis through the Entner-Doudoroff pathway with less ATP produced for lower biomass accumulation and higher product yield. When self-flocculated, the bacterial cells are more productive, since they can self-immobilize within bioreactors for high density, and are more tolerant to stresses for higher product titers, but this morphology needs to be controlled properly to avoid internal mass transfer limitation associated with their strong self-flocculation. Herewith we explored the regulation of cyclic diguanosine monophosphate (c-di-GMP) on self-flocculation of the bacterial cells through activating cellulose biosynthesis. While ZMO1365 and ZMO0919 with GGDEF domains for diguanylate cyclase activity catalyze c-di-GMP biosynthesis, ZMO1487 with an EAL domain for phosphodiesterase activity catalyzes c-di-GMP degradation, but ZMO1055 and ZMO0401 contain the dual domains with phosphodiesterase activity predominated. Since c-di-GMP is synthesized from GTP, the intracellular accumulation of this signal molecule through deactivating phosphodiesterase activity is preferred for activating cellulose biosynthesis to flocculate the bacterial cells, because such a strategy exerts less perturbance on intracellular processes regulated by GTP. These discoveries are significant for not only engineering unicellular Z. mobilis strains with the self-flocculating morphology to boost production but also understanding mechanism underlying c-di-GMP biosynthesis and degradation in the bacterium.

Use of yeast biocapsules as a fungal-based immobilized cell technology for Indian Pale Ale-type beer brewing

Immobilized cell technologies (ICT) have been used in wort fermentation, beer maturation, or production of alcohol-free or low-alcohol beer. The purpose of ICT is to restrict intact cells to a specific location while allowing biological function. It improves cell stability, operational flexibility, and control in brewing, as well as ease in executing continuous operations. We investigated the use of yeast biocapsules for Indian Pale Ale (IPA) type beer wort fermentation, a novel ICT in brewing. Yeast biocapsules are a spherical yeast immobilization system in which yeast cells are encapsulated and connected to the hyphae of an inactivated hollow filamentous fungus pellet. Fermentations with yeast encapsulated in alginate beads, as the standard immobilization practice, and in free (non-immobilized) forms were carried out in parallel. We found that yeast biocapsules are a better option for cell reutilization than alginate beads, but worse for beer must clarity. Beer brewed with yeast biocapsules differed in concentration for five volatile compounds (acetaldehyde, diacetyl, ethyl acetate, 1,1-diethoxyethane, and isoamyl alcohol) and three sensory characters (persistency of the foam, malt, and yeast character). KEY POINTS: • Yeast biocapsules were investigated for beer wort fermentation • Biocapsules improve cell reutilization but are limited for beer clarification • Beer brewed with biocapsules is chemically different than conventional beer • Most sensory features did not differ between biocapsule and control beer.

Deciphering Molecular Mechanism Underlying Self-Flocculation of Zymomonas mobilis for Robust Production

Zymomonas mobilis metabolizes sugar anaerobically through the Entner-Doudoroff pathway with less ATP generated for lower biomass accumulation to direct more sugar for product formation with improved yield, making it a suitable host to be engineered as microbial cell factories for producing bulk commodities with major costs from feedstock consumption. Self-flocculation of the bacterial cells presents many advantages, such as enhanced tolerance to environmental stresses, a prerequisite for achieving high product titers by using concentrated substrates. ZM401, a self-flocculating mutant developed from ZM4, the unicellular model strain of Z. mobilis, was employed in this work to explore the molecular mechanism underlying this self-flocculating phenotype. Comparative studies between ZM401 and ZM4 indicate that a frameshift caused by a single nucleotide deletion in the poly-T tract of ZMO1082 fused the putative gene with the open reading frame of ZMO1083, encoding the catalytic subunit BcsA of the bacterial cellulose synthase to catalyze cellulose biosynthesis. Furthermore, the single nucleotide polymorphism mutation in the open reading frame of ZMO1055, encoding a bifunctional GGDEF-EAL protein with apparent diguanylate cyclase/phosphodiesterase activities, resulted in the Ala526Val substitution, which consequently compromised in vivo specific phosphodiesterase activity for the degradation of cyclic diguanylic acid, leading to intracellular accumulation of the signaling molecule to activate cellulose biosynthesis. These discoveries are significant for engineering other unicellular strains from Z. mobilis with the self-flocculating phenotype for robust production. IMPORTANCE Stress tolerance is a prerequisite for microbial cell factories to be robust in production, particularly for biorefinery of lignocellulosic biomass to produce biofuels, bioenergy, and bio-based chemicals for sustainable socioeconomic development, since various inhibitors are released during the pretreatment to destroy the recalcitrant lignin-carbohydrate complex for sugar production through enzymatic hydrolysis of the cellulose component, and their detoxification is too costly for producing bulk commodities. Although tolerance to individual stress has been intensively studied, the progress seems less significant since microbial cells are inevitably suffering from multiple stresses simultaneously under production conditions. When self-flocculating, microbial cells are more tolerant to multiple stresses through the general stress response due to enhanced quorum sensing associated with the morphological change for physiological and metabolic advantages. Therefore, elucidation of the molecular mechanism underlying such a self-flocculating phenotype is significant for engineering microbial cells with the unique multicellular morphology through rational design to boost their production performance.

Manipulating cell flocculation-associated protein kinases in Saccharomyces cerevisiae enables improved stress tolerance and efficient cellulosic ethanol production

Cell self-flocculation endows yeast strains with improved environmental stress tolerance that benefits bioproduction. Exploration of the metabolic and regulatory network differences between the flocculating and non-flocculating cells is conducive to developing strains with satisfactory fermentation efficiency. In this work, integrated analyses of transcriptome, proteome, and phosphoproteome were performed using flocculating yeast Saccharomyces cerevisiae SPSC01 and its non-flocculating mutant grown under acetic acid stress, and the results revealed prominent changes in protein kinases. Overexpressing the mitogen-activated protein kinase Hog1 upregulated by flocculation led to reduced ROS accumulation and increased glutathione peroxidase activity, leading to improved ethanol production under stress. Among the seven genes encoding protein kinases that were tested, AKL1 showed the best performance when overexpressed, achieving higher ethanol productivity in both corncob hydrolysate and simulated corn stover hydrolysate. These results provide alternative strategies for improving cellulosic ethanol production by engineering key protein kinases in S. cerevisiae.

Very High Gravity Bioethanol Revisited: Main Challenges and Advances

Over the last decades, the constant growth of the world-wide industry has been leading to more and more concerns with its direct impact on greenhouse gas (GHG) emissions. Resulting from that, rising efforts have been dedicated to a global transition from an oil-based industry to cleaner biotechnological processes. A specific example refers to the production of bioethanol to substitute the traditional transportation fuels. Bioethanol has been produced for decades now, mainly from energy crops, but more recently, also from lignocellulosic materials. Aiming to improve process economics, the fermentation of very high gravity (VHG) mediums has for long received considerable attention. Nowadays, with the growth of multi-waste valorization frameworks, VHG fermentation could be crucial for bioeconomy development. However, numerous obstacles remain. This work initially presents the main aspects of a VHG process, giving then special emphasis to some of the most important factors that traditionally affect the fermentation organism, such as nutrients depletion, osmotic stress, and ethanol toxicity. Afterwards, some factors that could possibly enable critical improvements in the future on VHG technologies are discussed. Special attention was given to the potential of the development of new fermentation organisms, nutritionally complete culture media, but also on alternative process conditions and configurations.

From baker's yeast to genetically modified budding yeasts: the scientific evolution of bioethanol industry from sugarcane

The peculiarities of Brazilian fuel ethanol fermentation allow the entry of native yeasts that may dominate over the starter strains of Saccharomyces cerevisiae and persist throughout the sugarcane harvest. The switch from the use of baker's yeast as starter to selected budding yeasts obtained by a selective pressure strategy was followed by a wealth of genomic information that enabled the understanding of the superiority of selected yeast strains. This review describes how the process of yeast selection evolved in the sugarcane-based bioethanol industry, the selection criteria and recent advances in genomics that could advance the fermentation process. The prospective use of genetically modified yeast strains, specially designed for increased robustness and product yield, with special emphasis on those obtained by the CRISPR (clustered regularly interspaced palindromic repeats)-Cas9 (CRISPR-associated protein 9) genome-editing approach, is discussed as a possible solution to confer higher performance and stability to the fermentation process for fuel ethanol production.

The bubble-induced population dynamics of fermenting yeasts

Bubble-induced transport is a ubiquitous natural and industrial phenomenon. In brewery, such transport occurs due to gas bubbles generated through anaerobic fermentation by yeasts. Two major kinds of fermentation viz. top (ale) and bottom (lager) fermentation, display a difference in their yeast distributions inside a sugar broth. The reason for this difference is believed to be yeast-bubble adhesion arising due to surface hydrophobicity of the yeast cell wall; however, the physical mechanism is still largely a mystery. In this report, through in vivo experiments, we develop a novel theoretical model for yeast distribution based on the general conservation law. This work clarifies that bubble-induced diffusion is the dominant transport mechanism in bottom-fermentation by lagers whereas, yeast-bubble adhesion plays a leading role in transporting ales in top-fermentation, thereby corroborating the centuries-old belief regarding distribution difference in yeast population in two kinds of fermentation.

Genome sequencing, assembly, and annotation of the self-flocculating microalga Scenedesmus obliquus AS-6-11

BACKGROUND

Scenedesmus obliquus belongs to green microalgae and is widely used in aquaculture as feed, which is also explored for lipid production and bioremediation. However, genomic studies of this microalga have been very limited. Cell self-flocculation of microalgal cells can be used as a simple and economic method for harvesting biomass, and it is of great importance to perform genome-scale studies for the self-flocculating S. obliquus strains to promote their biotechnological applications.

RESULTS

We employed the Pacific Biosciences sequencing platform for sequencing the genome of the self-flocculating microalga S. obliquus AS-6-11, and used the MECAT software for de novo genome assembly. The estimated genome size of S. obliquus AS-6-11 is 172.3 Mbp with an N50 of 94,410 bp, and 31,964 protein-coding genes were identified. Gene Ontology (GO) and KEGG pathway analyses revealed 65 GO terms and 428 biosynthetic pathways. Comparing to the genome sequences of the well-studied green microalgae Chlamydomonas reinhardtii, Chlorella variabilis, Volvox carteri and Micractinium conductrix, the genome of S. obliquus AS-6-11 encodes more unique proteins, including one gene that encodes D-mannose binding lectin. Genes encoding the glycosylphosphatidylinositol (GPI)-anchored cell wall proteins, and proteins with fasciclin domains that are commonly found in cell wall proteins might be responsible for the self-flocculating phenotype, and were analyzed in detail. Four genes encoding both GPI-anchored cell wall proteins and fasciclin domain proteins are the most interesting targets for further studies.

CONCLUSIONS

The genome sequence of the self-flocculating microalgal S. obliquus AS-6-11 was annotated and analyzed. To our best knowledge, this is the first report on the in-depth annotation of the S. obliquus genome, and the results will facilitate functional genomic studies and metabolic engineering of this important microalga. The comparative genomic analysis here also provides new insights into the evolution of green microalgae. Furthermore, identification of the potential genes encoding self-flocculating proteins will benefit studies on the molecular mechanism underlying this phenotype for its better control and biotechnological applications as well.

Perspectives and new directions for bioprocess optimization using Zymomonas mobilis in the ethanol production

Zymomonas mobilis is an ethanologenic microbe that has a demonstrated potential for use in lignocellulosic biorefineries for bioethanol production. Z. mobilis exhibits a number of desirable characteristics for use as an ethanologenic microbe, with capabilities for metabolic engineering and bioprocess modification. Many advanced genetic tools, including mutation techniques, screening methods and genome editing have been successively performed to improve various Z. mobilis strains as potential consolidated ethanologenic microbes. Many bioprocess strategies have also been applied to this organism for bioethanol production. Z. mobilis biofilm reactors have been modified with various benefits, including high bacterial populations, less fermentation times, high productivity, high cell stability, resistance to the high concentration of substrates and toxicity, and higher product recovery. We suggest that Z. mobilis biofilm reactors could be used in bioethanol production using lignocellulosic substrates under batch, continuous and repeated batch processes.

Microalgal flocculation: Global research progress and prospects for algal biorefinery

Microalgal research has made significant progress due to versatile and high-value industrial applications of microalgal biomass or its derivatives. However, to explore their full potential and to achieve commercial robustness, microalgal biorefinery needs cost-effective technologies to produce, harvest, and process the microalgal biomass on large scale as higher production and harvesting cost is one of the key hindrances in the commercialization of algae-based products. Among several other algal biomass harvesting technologies, self-flocculation seems to be an attractive, low-cost, and eco-friendly harvesting technology. This review covers various flocculation-based methods that have been employed to harvest microalgal biomass with a special emphasis on self-flocculation in microalgae. Moreover, genetic engineering approaches to induce self-flocculation in non-flocculating microalgae along with the factors affecting self-flocculation and recent research trends have also been discussed. It is concluded that self-flocculation is the most desired approach for the energy- and environment-efficient harvesting of microalgal biomass. However, its poorly understood genetic basis needs to be deciphered through detailed studies to harness its potential for the algal biorefinery.

Cell Aggregation and Aerobic Respiration Are Important for Zymomonas mobilis ZM4 Survival in an Aerobic Minimal Medium

Zymomonas mobilis produces ethanol from glucose near the theoretical maximum yield, making it a potential alternative to the yeast Saccharomyces cerevisiae for industrial ethanol production. A potentially useful industrial feature is the ability to form multicellular aggregates called flocs, which can settle quickly and exhibit higher resistance to harmful chemicals than single cells. While spontaneous floc-forming Z. mobilis mutants have been described, little is known about the natural conditions that induce Z. mobilis floc formation or about the genetic factors involved. Here we found that wild-type Z. mobilis forms flocs in response to aerobic growth conditions but only in a minimal medium. We identified a cellulose synthase gene cluster and a single diguanylate cyclase that are essential for both floc formation and survival in a minimal aerobic medium. We also found that NADH dehydrogenase 2, a key component of the aerobic respiratory chain, is important for survival in a minimal aerobic medium, providing a physiological role for this enzyme, which has previously been found to be disadvantageous in a rich aerobic medium. Supplementation of the minimal medium with vitamins also promoted survival but did not inhibit floc formation.IMPORTANCE The bacterium Zymomonas mobilis is best known for its anaerobic fermentative lifestyle, in which it converts glucose into ethanol at a yield surpassing that of yeast. However, Z. mobilis also has an aerobic lifestyle, which has confounded researchers with its attributes of poor growth, accumulation of toxic acetic acid and acetaldehyde, and respiratory enzymes that are detrimental for aerobic growth. Here we show that a major Z. mobilis respiratory enzyme and the ability to form multicellular aggregates, called flocs, are important for survival, but only during aerobic growth in a medium containing a minimum set of nutrients required for growth. Supplements, such as vitamins or yeast extract, promote aerobic growth and, in some cases, inhibit floc formation. We propose that Z. mobilis likely requires aerobic respiration and floc formation in order to survive in natural environments that lack protective factors found in supplements such as yeast extract.

Repeated ethanol fermentation from membrane-concentrated sweet sorghum juice using the flocculating yeast Saccharomyces cerevisiae F118 strain

The aim of this study was to construct a cost-effective method for repeated bioethanol production using membrane (ultrafiltration permeation and nanofiltration concentration)-concentrated sweet sorghum juice by using flocculent Saccharomyces cerevisiae F118 strain. With low initial dry cell concentrations at around 0.28-0.35 g L^-1, the S. cerevisiae F118 strain provided an ethanol titer of 86.19 ± 1.15 g L^-1 (theoretical ethanol yield of 70.77%), which was higher than the non-flocculent S. cerevisiae BY4741 strain at 33.92 ± 0.99 g L^-1 after 24 h fermentation. This result was correlated with higher gene expressions of the sucrose-hydrolysing enzyme invertase, sugar phosphorylation, and pyruvate-to-ethanol pathways in the F118 strain compared with the BY4741 strain. Sequential fed-batch fermentation was conducted, and the F118 strain was easily separated from the fermentation broth via the formation of flocs and sediment. After the 5th cycle of fermentation with the F118 strain, the ethanol concentration reached 100.37 g L^-1.

Contribution of cellulose synthesis, formation of fibrils and their entanglement to the self-flocculation of Zymomonas mobilis

Due to the unique Entner-Doudoroff pathway, Zymomonas mobilis has been acknowledged as a potential host to be engineered for biorefinery to produce biofuels and biobased chemicals. The self-flocculation of Z. mobilis can make the bacterial cells self-immobilized within bioreactors for high density to improve product productivities, and in the meantime enhance their tolerance to stresses, particularly product inhibition and the toxicity of byproducts released during the pretreatment of lignocellulosic biomass. In this work, we explored mechanism underlying such a phenotype with the self-flocculating strain ZM401 developed from the regular non-flocculating strain ZM4. Cellulase de-flocculation and the restoration of the self-flocculating phenotype for the de-flocculated bacterial cells subjected to culture confirmed the essential role of cellulose biosynthesis in the self-flocculation of ZM401. Furthermore, the deactivation of both Type I and Type IV restriction-modification systems was performed for ZM4 and ZM401 to improve their transformation efficiencies. Comparative genome analysis detected the deletion of a thymine from ZMO1082 in ZM401, leading to a frame-shift mutation for the putative gene to be integrated into the neighboring downstream gene ZMO1083 encoding the catalytic subunit A of cellulose synthase, and consequently created a new gene to encode a larger transmembrane protein BcsA_401 for more efficient synthesis of cellulose as well as the development of cellulose fibrils and their entanglement for the self-flocculation of the mutant. These speculations were confirmed by the morphological observation of the bacterial cells under scanning electron microscopy, the impact of the gene deletion on the self-flocculation of ZM401, and the restoration of the self-flocculating phenotype of ZM401 ΔbcsA by the gene complementation. The progress will lay a foundation not only for fundamental research in deciphering molecular mechanisms underlying the self-flocculation of Z. mobilis and stress tolerance associated with the morphological change but also for technological innovations in engineering non-flocculating Z. mobilis and other bacterial species with the self-flocculating phenotype.

A novel chimaeric flocculation protein enhances flocculation in Saccharomyces cerevisiae

Yeast flocculation is the reversible formation of multicellular complexes mediated by lectin-like cell wall proteins binding to neighbouring cells. Strong flocculation can improve the inhibitor tolerance and fermentation performance of yeast cells in second generation bioethanol production. The strength of flocculation increases with the size of the flocculation protein and is strain dependent. However, the large number of internal repeats in the sequence of FLO1 from Saccharomyces cerevisiae S288c makes it difficult to recombinantly express the gene to its full length. In the search for novel flocculation genes resulting in strong flocculation, we discovered a DNA sequence, FLONF, that gives NewFlo phenotype flocculation in S. cerevisiae CEN.PK 113-7D. The nucleotide sequence of the internal repeats of FLONF differed from those of FLO1. We hypothesized that a chimaeric flocculation gene made up of a FLO1 variant derived from S. cerevisiae S288c and additional repeats from FLONF from S. cerevisiae CCUG 53310 would be more stable and easier to amplify by PCR. The constructed gene, FLOw, had 22 internal repeats compared to 18 in FLO1. Expression of FLOw in otherwise non-flocculating strains led to strong flocculation. Despite the length of the gene, the cassette containing FLOw could be easily amplified and transformed into yeast strains of different genetic background, leading to strong flocculation in all cases tested. The developed gene can be used as a self-immobilization technique or to obtain rapidly sedimenting cells for application in e.g. sequential batches without need for centrifugation.

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A novel gene sequence conferring NewFlo phenotype flocculation was isolated.

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The chimaeric gene FLOw was constructed from parts of FLO1 and FLONF.

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Overexpression of FLOw gave strong flocculation in several S. cerevisiae strains.

Genome Sequence of the Self-Flocculating Strain Saccharomyces cerevisiae SPSC01

The self-flocculation of yeast cells presents advantages for continuous ethanol fermentation such as their self-immobilization within fermenters for high density to improve ethanol productivity and cost-effective biomass recovery by gravity sedimentation. We sequenced and analyzed the genome of the self-flocculating Saccharomyces cerevisiae SPSC01 for the industrial production of fuel ethanol.

Genetic characterization and modification of a bioethanol-producing yeast strain

Yeast Saccharomyces cerevisiae strains isolated from different sources generally show extensive genetic and phenotypic diversity. Understanding how genomic variations influence phenotypes is important for developing strategies with improved economic traits. The diploid S. cerevisiae strain NY1308 is used for cellulosic bioethanol production. Whole genome sequencing identified an extensive amount of single nucleotide variations and small insertions/deletions in the genome of NY1308 compared with the S288c genome. Gene annotation of the assembled NY1308 genome showed that 43 unique genes are absent in the S288c genome. Phylogenetic analysis suggested most of the unique genes were obtained through horizontal gene transfer from other species. RNA-Seq revealed that some unique genes were not functional in NY1308 due to unidentified intron sequences. During bioethanol fermentation, NY1308 tends to flocculate when certain inhibitors (derived from the pretreatment of cellulosic feedstock) are present in the fermentation medium. qRT-PCR and genetic manipulation confirmed that the novel gene, NYn43, contributed to the flocculation ability of NY1308. Deletion of NYn43 resulted in a faster fermentation rate for NY1308. This work disclosed the genetic characterization of a bioethanol-producing S. cerevisiae strain and provided a useful paradigm showing how the genetic diversity of the yeast population would facilitate the personalized development of desirable traits.

Recent advances in yeast cell-surface display technologies for waste biorefineries

Waste biorefinery aims to maximize the output of value-added products from various artificial/agricultural wastes by using integrated bioprocesses. To make waste biorefinery economically feasible, it is thus necessary to develop a low-cost, environment-friendly technique to perform simultaneous biodegradation and bioconversion of waste materials. Cell-surface display engineering is a novel, cost-effective technique that can auto-immobilize proteins on the cell exterior of microorganisms, and has been applied for use with waste biofinery. Through tethering different enzymes (e.g., cellulase, lipase, and protease) or metal-binding peptides on cell surfaces, various yeast strains can effectively produce biofuels and biochemicals from sugar/protein-rich waste materials, catalyze waste oils into biodiesels, or retrieve heavy metals from wastewater. This review critically summarizes recent applications of yeast cell-surface display on various types of waste biorefineries, highlighting its potential and future challenges with regard to commercializing this technology.

Development of stress tolerant Saccharomyces cerevisiae strains by metabolic engineering: New aspects from cell flocculation and zinc supplementation

Budding yeast Saccharomyces cerevisiae is widely studied for the production of biofuels from lignocellulosic biomass. However, economic production is currently challenged by the repression of cell growth and compromised fermentation performance of S. cerevisiae strains in the presence of various environmental stresses, including toxic level of final products, inhibitory compounds released from the pretreatment of cellulosic feedstocks, high temperature, and so on. Therefore, it is important to improve stress tolerance of S. cerevisiae to these stressful conditions to achieve efficient and economic production. In this review, the latest advances on development of stress tolerant S. cerevisiae strains are summarized, with the emphasis on the impact of cell flocculation and zinc addition. It was found that cell flocculation affected ethanol tolerance and acetic acid tolerance of S. cerevisiae, and addition of zinc to a suitable level improved stress tolerance of yeast cells to ethanol, high temperature and acetic acid. Further studies on the underlying mechanisms by which cell flocculation and zinc status affect stress tolerance will not only enrich our knowledge on stress response and tolerance mechanisms of S. cerevisiae, but also provide novel metabolic engineering strategies to develop robust yeast strains for biofuels production.

Expression of AtMed15 of Arabidopsis in yeast causes flocculation and increases ethanol production in yeast culture

Mediator, a multiprotein complex involved in transcription of class II genes, was first discovered in yeast and then characterized in many metazoans revealing a striking structural conservation of the complex. However, sequences of Mediator subunits are not well conserved raising a question on the functional conservation of these individual subunits. In this study, expression of Med15 of Arabidopsis (AtMed15) in gal11∆ yeast could not complement the function of ScGal11 in galactose metabolism and resistance against cycloheximide. Surprisingly, AtMed15 changed the morphology of the yeast cells. The cells adhered strongly on the surface of the agar media, and showed robust flocculation in the liquid media without affecting the growth. The AtMed15-induced adhesion and flocculation were observed in different carbon sources. Calcium-assisted cell wall-bound mannan-binding proteins were found to be involved in this flocculation, which was unaffected by wide fluctuation of pH or temperatures revealing its constitutive robust nature. Expression of few flocculation related Flo genes was up-regulated in these cells. Interestingly, there was significant increase in ethanol production by the yeast expressing AtMed15. Robust and constitutive flocculation and increased ethanol production by yeast cells harbouring AtMed15 indicate an opportunity of its important usage in biotechnology industries.

Redox potential driven aeration during very-high-gravity ethanol fermentation by using flocculating yeast

Ethanol fermentation requires oxygen to maintain high biomass and cell viability, especially under very-high-gravity (VHG) condition. In this work, fermentation redox potential (ORP) was applied to drive the aeration process at low dissolved oxygen (DO) levels, which is infeasible to be regulated by a DO sensor. The performance and characteristics of flocculating yeast grown under 300 and 260 g glucose/L conditions were subjected to various aeration strategies including: no aeration; controlled aeration at -150, -100 and -50 mV levels; and constant aeration at 0.05 and 0.2 vvm. The results showed that anaerobic fermentation produced the least ethanol and had the highest residual glucose after 72 h of fermentation. Controlled aerations, depending on the real-time oxygen demand, led to higher cell viability than the no-aeration counterpart. Constant aeration triggered a quick biomass formation, and fast glucose utilization. However, over aeration at 0.2 vvm caused a reduction of final ethanol concentration. The controlled aeration driven by ORP under VHG conditions resulted in the best fermentation performance. Moreover, the controlled aeration could enhance yeast flocculating activity, promote an increase of flocs size, and accelerate yeast separation near the end of fermentation.

Biofuel Production Based on Carbohydrates from Both Brown and Red Macroalgae: Recent Developments in Key Biotechnologies

Marine macroalgae (green, red and brown macroalgae) have attracted attention as an alternative source of renewable biomass for producing both fuels and chemicals due to their high content of suitable carbohydrates and to their advantages over terrestrial biomass. However, except for green macroalgae, which contain relatively easily-fermentable glucans as their major carbohydrates, practical utilization of red and brown macroalgae has been regarded as difficult due to the major carbohydrates (alginate and mannitol of brown macroalgae and 3,6-anhydro-L-galactose of red macroalgae) not being easily fermentable. Recently, several key biotechnologies using microbes have been developed enabling utilization of these brown and red macroalgal carbohydrates as carbon sources for the production of fuels (ethanol). In this review, we focus on these recent developments with emphasis on microbiological biotechnologies.

Current progress in high cell density yeast bioprocesses for bioethanol production

High capital costs and low reaction rates are major challenges for establishment of fermentation-based production systems in the bioeconomy. Using high cell density cultures is an efficient way to increase the volumetric productivity of fermentation processes, thereby enabling faster and more robust processes and use of smaller reactors. In this review, we summarize recent progress in the application of high cell density yeast bioprocesses for first and second generation bioethanol production. High biomass concentrations obtained by retention of yeast cells in the reactor enables easier cell reuse, simplified product recovery and higher dilution rates in continuous processes. High local cell density cultures, in the form of encapsulated or strongly flocculating yeast, furthermore obtain increased tolerance to convertible fermentation inhibitors and utilize glucose and other sugars simultaneously, thereby overcoming two additional hurdles for second generation bioethanol production. These effects are caused by local concentration gradients due to diffusion limitations and conversion of inhibitors and sugars by the cells, which lead to low local concentrations of inhibitors and glucose. Quorum sensing may also contribute to the increased stress tolerance. Recent developments indicate that high cell density methodology, with emphasis on high local cell density, offers significant advantages for sustainable second generation bioethanol production.

Current progress and future prospect of microalgal biomass harvest using various flocculation technologies

Microalgae have been extensively studied for the production of various valuable products. Application of microalgae for the production of renewable energy has also received increasing attention in recent years. However, high cost of microalgal biomass harvesting is one of the bottlenecks for commercialization of microalgae-based industrial processes. Considering harvesting efficiency, operation economics and technological feasibility, flocculation is a superior method to harvest microalgae from mass culture. In this article, the latest progress of various microalgal cell harvesting methods via flocculation is reviewed with the emphasis on the current progress and prospect in environmentally friendly bio-based flocculation. Harvesting microalgae through bio-based flocculation is a promising component of the low-cost microalgal biomass production technology.

Characteristics of Saccharomyces cerevisiae yeasts exhibiting rough colonies and pseudohyphal morphology with respect to alcoholic fermentation

Among the native yeasts found in alcoholic fermentation, rough colonies associated with pseudohyphal morphology belonging to the species Saccharomyces cerevisiae are very common and undesirable during the process. The aim of this work was to perform morphological and physiological characterisations of S. cerevisiae strains that exhibited rough and smooth colonies in an attempt to identify alternatives that could contribute to the management of rough colony yeasts in alcoholic fermentation. Characterisation tests for invasiveness in Agar medium, killer activity, flocculation and fermentative capacity were performed on 22 strains (11 rough and 11 smooth colonies). The effects of acid treatment at different pH values on the growth of two strains (“52” - rough and “PE-02” - smooth) as well as batch fermentation tests with cell recycling and acid treatment of the cells were also evaluated. Invasiveness in YPD Agar medium occurred at low frequency; ten of eleven rough yeasts exhibited flocculation; none of the strains showed killer activity; and the rough strains presented lower and slower fermentative capacities compared to the smooth strains in a 48-h cycle in a batch system with sugar cane juice. The growth of the rough strain was severely affected by the acid treatment at pH values of 1.0 and 1.5; however, the growth of the smooth strain was not affected. The fermentative efficiency in mixed fermentation (smooth and rough strains in the same cell mass proportion) did not differ from the efficiency obtained with the smooth strain alone, most likely because the acid treatment was conducted at pH 1.5 in a batch cell-recycle test. A fermentative efficiency as low as 60% was observed with the rough colony alone.

Ethanol fermentation of energy beets by self-flocculating and non-flocculating yeasts

Specialized varieties of sugar beets (Energy Beets™) are being developed for producing industrial sugars in Arkansas' Mississippi River Delta. To evaluate their suitability for producing regional fermentation feedstocks, we report initial cultivation trials and ethanol fermentation of raw beet juice and combined juice with pulp mash (JPM) liquefied with enzymes, comparing ethanol yields under different regimes by self-flocculating and non-flocculating yeasts. Nine varieties produced root yields averaging 115Mg/ha and 18.5% sucrose contents. Raw beet juice fermentation yielded ethanol up to 0.48g/g (sugar). JPM was directly fermented through either a sequential (SeqSF) or simultaneous saccharification and fermentation (SSF) process. For both yeast types, SSF was a more efficient process than SeqSF, with ethanol yields up to 0.47g/g (sugar) and volumetric productivity up to 7.81g/L/h. These results indicate the self-flocculating yeast is suitable for developing efficient bioprocesses to ferment industrial sugar from energy beets.

Digital and analog gene circuits for biotechnology

Biotechnology offers the promise of valuable chemical production via microbial processing of renewable and inexpensive substrates. Thus far, static metabolic engineering strategies have enabled this field to advance industrial applications. However, the industrial scaling of statically engineered microbes inevitably creates inefficiencies due to variable conditions present in large-scale microbial cultures. Synthetic gene circuits that dynamically sense and regulate different molecules can resolve this issue by enabling cells to continuously adapt to variable conditions. These circuits also have the potential to enable next-generation production programs capable of autonomous transitioning between steps in a bioprocess. Here, we review the design and application of two main classes of dynamic gene circuits, digital and analog, for biotechnology. Within the context of these classes, we also discuss the potential benefits of digital-analog interconversion, memory, and multi-signal integration. Though synthetic gene circuits have largely been applied for cellular computation to date, we envision that utilizing them in biotechnology will enhance the efficiency and scope of biochemical production with living cells.

Characterization of the flocculating agent from the spontaneously flocculating microalga Chlorella vulgaris JSC-7

High cost of biomass recovery is one of the bottlenecks for developing cost-effective processes with microalgae, particularly for the production of biofuels and bio-based chemicals through biorefinery, and microalgal biomass recovery through cell flocculation is a promising strategy. Some microalgae are naturally flocculated whose cells can be harvested by simple sedimentation. However, studies on the flocculating agents synthesized by microalgae cells are still very limited. In this work, the cell flocculation of a spontaneously flocculating microalga Chlorella vulgaris JSC-7 was studied, and the flocculating agent was identified to be cell wall polysaccharides whose crude extract supplemented at low dosage of 0.5 mg/L initiated the more than 80% flocculating rate of freely suspended microalgae C. vulgaris CNW11 and Scenedesmus obliquus FSP. Fourier transform infrared (FTIR) analysis revealed a characteristic absorption band at 1238 cm(-1), which might arise from PO asymmetric stretching vibration of [Formula: see text] phosphodiester. The unique cell wall-associated polysaccharide with molecular weight of 9.86×10(3) g/mol, and the monomers consist of glucose, mannose and galactose with a molecular ratio of 5:5:2. This is the first time to our knowledge that the flocculating agent from C. vulgaris has been characterized, which could provide basis for understanding the cell flocculation of microalgae and breeding of novel flocculating microalgae for cost-effective biomass harvest.

Multi-stage continuous high cell density culture systems: a review

A multi-stage continuous high cell density culture (MSC-HCDC) system makes it possible to achieve high productivity together with high product titer of many bioproducts. For long-term continuous operation of MSC-HCDC systems, the cell retention time and hydraulic retention time must be decoupled and strains (bacteria, yeast, plant, and animal cells) must be stable. MSC-HCDC systems are suitable for low-value high-volume extracellular products such as fuel ethanol, lactic acid or volatile fatty acids, and high-value products such as monoclonal antibodies as well as intracellular products such as polyhydroxybutyric acid (PHB), microbial lipids or a number of therapeutics. Better understanding of the fermentation kinetics of a specific product and reliable high-density culture methods for the product-generating microorganisms will facilitate timely industrialization of MSC-HCDC systems for products that are currently obtained in fed-batch bioreactors.

Studying the rapid bioconversion of lignocellulosic sugars into ethanol using high cell density fermentations with cell recycle

BACKGROUND

The Rapid Bioconversion with Integrated recycle Technology (RaBIT) process reduces capital costs, processing times, and biocatalyst cost for biochemical conversion of cellulosic biomass to biofuels by reducing total bioprocessing time (enzymatic hydrolysis plus fermentation) to 48 h, increasing biofuel productivity (g/L/h) twofold, and recycling biocatalysts (enzymes and microbes) to the next cycle. To achieve these results, RaBIT utilizes 24-h high cell density fermentations along with cell recycling to solve the slow/incomplete xylose fermentation issue, which is critical for lignocellulosic biofuel fermentations. Previous studies utilizing similar fermentation conditions showed a decrease in xylose consumption when recycling cells into the next fermentation cycle. Eliminating this decrease is critical for RaBIT process effectiveness for high cycle counts.

RESULTS

Nine different engineered microbial strains (including Saccharomyces cerevisiae strains, Scheffersomyces (Pichia) stipitis strains, Zymomonas mobilis 8b, and Escherichia coli KO11) were tested under RaBIT platform fermentations to determine their suitability for this platform. Fermentation conditions were then optimized for S. cerevisiae GLBRCY128. Three different nutrient sources (corn steep liquor, yeast extract, and wheat germ) were evaluated to improve xylose consumption by recycled cells. Capacitance readings were used to accurately measure viable cell mass profiles over five cycles.

CONCLUSION

The results showed that not all strains are capable of effectively performing the RaBIT process. Acceptable performance is largely correlated to the specific xylose consumption rate. Corn steep liquor was found to reduce the deleterious impacts of cell recycle and improve specific xylose consumption rates. The viable cell mass profiles indicated that reduction in specific xylose consumption rate, not a drop in viable cell mass, was the main cause for decreasing xylose consumption.

Evaluation of sweet potato for fuel bioethanol production: hydrolysis and fermentation

The enzymatic starch hydrolysis and bioethanol production from a variety of sweet potato developed for bioenergy purposes (K 9807.1) on the basis of its high starch yields, was studied. Drying at 55°C and 95°C of sweet potato neither affected the sugar content nor the starch enzymatic hydrolysis efficiency. Simultaneous saccharification and ethanol fermentations for dry matter ratio of sweet potato to water from 1:8 to 1:2 (w/v) were studied. Fresh sweet potato and dried at 55°C (flour) were assayed. At ratios of 1:8, similar results for fresh sweet potato and flour in terms of ethanol concentration (38-45 g/L), fermentation time (16 h) and sugar conversion (~ 100%) were found. At higher dry matter content, faster full conversion were observed using flour. A higher ratio than that for fresh sweet potato (1:2.2) did not improve the final ethanol concentration (100 g/L) and yields. High ethanol yields were found for VHG (very high gravity) conditions. The sweet potato used is an attractive raw matter for fuel ethanol, since up to 4800 L ethanol per hectare can be obtained.

Improved efficiency of butanol production by absorbent fermentation with a renewable carrier

BACKGROUND

Biobutanol production is still not economically competitive because of some principal drawbacks including high cost in feedstock consumption, low butanol concentration in the fermentation broth caused by severe product inhibition. An alternative fermentation mode is becoming an urgent requirement to solve these problems. Biobutanol production by absorbent fermentation with a renewable carrier, i.e. pretreated straw materials, is studied in this paper.

RESULTS

Compared with other types of porous media, alkali-treated steam-exploded straw was proved to be a suitable carrier for absorbent fermentation of butanol. The Acetone-Butanol-Ethanol (ABE) concentration increased by 52% compared with submerged culture at an initial glucose concentration of 65 g/L. The adsorption of ABE solvent on substrate and increased bacterial concentration alleviated the end product inhibition and partly explained this positive effect. The steam pretreatment conditions, solid-liquid ratio, substrate types and substrate concentration were also investigated. Steam-explosion at 1.1 MPa for 4 min and solid-liquid ratio of 1:10 was shown to be the optimum. Glucose showed a great advantage over xylose, and higher glucose content was more conducive to biobutanol production. However, the yield of solvent decreased with the increased initial sugar concentration. Considering comprehensively, 100 g/L initial glucose was considered to be the optimum.

CONCLUSIONS

This work demonstrated an effective approach of improved butanol fermentation and its probable mechanisms of this positive effect, i.e. the adsorption of ABE solvent and the adhesion of bacteria on porous substrate accounted for the production improvement and the proportional variation of solvent constituents.

Biosorption of Elements

Biosorption is a unique ability of living or dead biomass to interact with substances such as metals where reduction of sorbate concentration can be achieved. Thus, it has been widely proposed as a promising alternative for metal remediation and recovery owing to its low cost and sustainable “green” nature. Despite considerable biosorption‐related research performed in the past few decades, no significant commercial success has been achieved so far. This chapter starts with discussion of the basic science of biosorption and the potential of some selected biomasses such as yeast, algae, agro‐based waste and vermicompost to be used as biosorbent material. Following this, some important issues regarding the practical application of biosorption are highlighted, including the advantages and disadvantages of using dead or living biomass, the availability of biosorption reactors, immobilization techniques, metal recovery and post‐treatment of spent biosorbent. Lastly, current challenges that limit the commercial success of biosorption as well as the direction of future research are discussed.